We examined a complete list of South American mussels (Mytilidae) to identify species with current or potential needs for management and conservation actions. Based on ecological/ecosystem (aggregations, beds or banks affecting ecosystem functioning) and socio-economic (artisanal fisheries or aquaculture systems) attributes species with high relevance were identified. At least 14 species exhibited large ecosystem level effects at local scales. Further, most of them also sustain important fisheries: nearly one/third of these fisheries showed characteristics that may contribute to their lack of sustainability and overexploitation, while half are either in the initial exploitation phase or in the stabilization of extraction and institutionalization phase. Invading species are modifying the structure of mussel habitats. Allocation of spatially explicit management tools, notably Territorial User Rights in Fisheries and Marine Reserves, together with co-management initiatives, are suggested as relevant tools to fulfill management and conservation objectives for these key bioengineering species.